JSON files for visualizing source trees aligned to taxonomies in Phylografter.
Example Setup 1:
Quick and easy method to grab the JSON files and put them into the correct location with Git.
- Download the taxonomy-stree-json project. The easiest way to do this is change directories to your /path/to/phylografter/static directory, and do a
git clone https://github.com/OpenTreeOfLife/taxonomy-stree-json. This will clone the entire repository where it needs to be in Phylografter.
- Add this directory to your .gitignore IF you are using git to manage Phylografter, so that you can manage this repo independently.
Example Setup 2:
This method shows how to create a sym-link in the
phylografter/static directory so that you can keep the JSON files in whatever location you prefer.
- Download the entire repository.
- Open up terminal:
- Unzip the repo into a directory of your choice:
unzip taxonomy-stree-json-master.zip -d destination_folder
- Switch into the phylografter static directory:
- Create a symbolic link to your taxonomy-stree-json directory:
ln -s /full/path/to/taxonomy-stree-json ..
If you prefer, you can use the pipeline in the scripts folder to generate your own, more recently updated versions of the JSON files. As a warning though, generating the treecache files and the JSON documents can take quite a bit of time.
You can also use any combination of these approaches, such as
git clone the repo into your home directory, and then creating the sym-link to that directory as described in Example Setup 2. Ultimately, as long as the directory is named
taxonomy-stree-json, and it is in or linked from the
phylografter/static directory it should all work.